Hey,

1 I installed Galaxy locally.
2 I also have BWA installed and then used the 
3 shed repository to get the bwa wrapper.
4 I have the reference genome:
-rw-r--r-- 1 trr users      10509 2013-07-25 11:31 human_g1k_v37.dict
-rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fasta
-rw-r--r-- 1 trr users       6597 2013-07-25 19:41 human_g1k_v37.fasta.amb
-rw-r--r-- 1 trr users       6844 2013-07-25 19:41 human_g1k_v37.fasta.ann
-rw-r--r-- 1 trr users 3101804844 2013-07-25 19:41 human_g1k_v37.fasta.bwt
-rw-r--r-- 1 trr users       2746 2013-07-25 11:32 human_g1k_v37.fasta.fai
-rw-r--r-- 1 trr users  775451186 2013-07-25 19:41 human_g1k_v37.fasta.pac
-rw-r--r-- 1 trr users 1550902424 2013-07-25 20:02 human_g1k_v37.fasta.sa
 
5 and I changed the bwa_index and bw_index_color.loc to the path
/genedata/human_genome_GRCh37/hg19.fa

6 This is my $PATH
trr@portalmoritz:~> echo $PATH
/home/trr/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/home/trr/bpipe-0.9.8/bin:/home/trr/bwa-0.7.5a:/home/trr/samtools-0.1.19

Is there anything I am missing? I would be glad about some help.
Best
Moritz